This project will chart with high-resolution the genetic pathways that give rise to defined clinica phenotypes. We will utilize the power of the hybrid mouse diversity panel (HMDP), combined with massive-scale RNA sequencing and proteomics, to trace the interconnections from DNA to RNA to protein and provide layered information on the production of medically relevant traits. The HMDP consists of 100 inbred and recombinant inbred strains. The panel has a wide array of meiotic breakpoints and has been densely genotyped with more than 140,000 single nucleotide polymorphisms (SNPs), allowing very fine mapping of quantitative trait loci (QTLs). In addition, the HMDP is genetically stable and renewable and can be assayed for multiple phenotypes, yielding cumulative biological information. We will expand our previous HMDP-based studies of metabolic and behavioral disorders, adding massive-scale RNA sequencing (RNA-Seq) and proteomics to detail genetic control of protein expression. Our approach offers the distinct advantage of mapping loci for known pathways as well as variant RNA and protein species. The following aims are proposed: (1) We will perform RNA-Seq on liver tissue to illuminate metabolic disease and on hippocampal tissue to investigate variations in learning and memory. (2) We will perform mass spectrometry to survey the proteome of the hippocampus. (Our data on liver proteomics has already been published.) (3) The combined datasets will be analyzed with powerful statistical tools to understand the genetic regulation of transcript and protein expression. These studies will map genetic networks and inter-tissue regulatory pathways for clinical traits and suggest new, highly specific therapeutic strategies.